Complementary hydrophobic interaction of the redox enzyme maturation protein NarJ with the signal peptide of the respiratory nitrate reductase NarG.

In bacteria, NarJ plays an essential role as a redox enzyme maturation protein in the assembly of the nitrate reductase NarGHI by interacting with the N-terminal signal peptide of NarG to facilitate cofactor incorporation into NarG. The purpose of our research was to elucidate the exact mechanism of NarG signal peptide recognition by NarJ. We determined the structures of NarJ alone and in complex with the signal peptide of NarG via X-ray crystallography and verified the NarJ-NarG interaction through mutational, binding, and molecular dynamics simulation studies. NarJ adopts a curved α-helix bundle structure with a U-shaped hydrophobic groove on its concave side. This groove accommodates the signal peptide of NarG via a dual binding mode in which the left and right parts of the NarJ groove each interact with two consecutive hydrophobic residues from the N- and C-terminal regions of the NarG signal peptide, respectively, through shape and chemical complementarity. This binding is accompanied by unwinding of the helical structure of the NarG signal peptide and by stabilization of the NarG-binding loop of NarJ. We conclude that NarJ recognizes the NarG signal peptide through a complementary hydrophobic interaction mechanism that mediates a structural rearrangement.

Critical Role of Surface Termination of Sapphire Substrates in Crystallographic Epitaxial Growth of MoS2 Using Inorganic Molecular Precursors.

A highly reproducible route for the epitaxial growth of single-crystalline monolayer MoS2 on a C-plane sapphire substrate was developed using vapor-pressure-controllable inorganic molecular precursors MoOCl4 and H2S. Microscopic, crystallographic, and spectroscopic analyses indicated that the epitaxial MoS2 film possessed outstanding electrical and optical properties, excellent homogeneity, and orientation selectivity. The systematic investigation of the effect of growth temperature on the crystallographic orientations of MoS2 revealed that the surface termination of the sapphire substrate with respect to the growth temperature determines the crystallographic orientation selectivity of MoS2. Our results suggest that controlling the surface to form a half-Al-terminated surface is a prerequisite for the epitaxial growth of MoS2 on a C-plane sapphire substrate. The insights on the growth mechanism, especially the significance of substrate surface termination, obtained through this study will aid in designing efficient epitaxial growth routes for developing single-crystalline monolayer transition metal dichalcogenides.

Growth of Monolayer and Multilayer MoS2 Films by Selection of Growth Mode: Two Pathways via Chemisorption and Physisorption of an Inorganic Molecular Precursor.

We report facile growth methods for high-quality monolayer and multilayer MoS2 films using MoOCl4 as the vapor-phase molecular Mo precursor. Compared to the conventional covalent solid-type Mo precursors, the growth pressure of MoOCl4 can be precisely controlled. This enables the selection of growth mode by adjusting growth pressure, which facilitates the control of the growth behavior as the growth termination at a monolayer or as the continuous growth to a multilayer. In addition, the use of carbon-free precursors eliminates concerns about carbon contamination in the produced MoS2 films. Systematic studies for unveiling the growth mechanism proved two growth modes, which are predominantly the physisorption and chemisorption of MoOCl4. Consequently, the thickness of MoS2 can be controlled by our method as the application demands.

Association of inferior vena cava diameter ratio measured on computed tomography scans with the outcome of patients with septic shock.

The collapsibility and diameter of the inferior vena cava (IVC) are known to predict the volume state in critically ill patients. However, no study has examined the prognostic value of the IVC diameter ratio measured on computed tomography (CT) in patients with septic shock. A retrospective observational study was conducted on adult septic shock patients visiting the emergency department at a university hospital in Korea. The IVC diameter ratio was calculated by dividing the maximal transverse and anteroposterior diameters. Multivariable logistic regression analysis was conducted to investigate whether the IVC diameter ratio predicted in-hospital mortality. The area under the curve (AUC) was calculated, and the sensitivity, specificity, positive predictive value, and negative predictive value with the cut-off values were computed. A total of 423 adult septic shock patients were included, and the in-hospital mortality rate was 17%. The median IVC diameter ratio in non-survivors was significantly greater than in survivors (1.56 cm vs 1.4 cm, P = .004). The IVC diameter ratio was found to be significantly associated with in-hospital mortality on multivariate logistic regression analysis after adjustment for confounding variables (odds ratio = 1.48, confidence interval: 1.097-1.998, P = 0.01). The AUC for IVC diameter ratio was 0.607. A cut-off IVC diameter ratio of ≥1.31 cm had 75% sensitivity and 42% specificity for predicting in-hospital mortality. The IVC diameter ratio measured on CT may to be helpful in predicting the prognosis of septic shock patients. However, due to its low diagnostic performance and sensitivity, further research is warranted.

TLR5 binding and activation by KMRC011, a flagellin-derived radiation countermeasure.

Entolimod (CBLB502) is a flagellin-derived radiation countermeasure currently under clinical trial. Entolimod exerts radioprotective activity by directly interacting with TLR5, an innate immune receptor, using the conserved domains of flagellin. Entolimod was designed to contain an artificially introduced N-terminal region that is not related to drug effects and might trigger unexpected toxic immunogenic reactions in humans. To refine the entolimod drug design, we engineered entolimod into KMRC011 by removing its ancillary region. The TLR5 binding and activating capacities of KMRC011 were assessed through biophysical and cellular analyses. KMRC011 forms an exceptionally stable complex with TLR5 at a 1:1 molar ratio with an equilibrium dissociation constant of ∼100 pM and potently activates TLR5. Moreover, alanine scanning mutagenesis identified the R90 and E114 residues of KMRC011 as a TLR5 activation hotspot. Further comparative analysis demonstrated that KMRC011 binds and activates TLR5 in a mode similar to that of entolimod. Thus, we propose that KMRC011 can be used in place of entolimod as a second-generation radiation countermeasure that shows none of the immunogenic side effects derived from the entolimod ancillary region.

Helicobacter pylori flagellin: TLR5 evasion and fusion-based conversion into a TLR5 agonist.

Helicobacter pylori is a flagellated bacterium of the Epsilonproteobacteria class that causes peptic ulcers. Flagellin is a primary structural protein that assembles into the flagellar filament. Flagellins from bacteria that belong to the Gammaproteobacteria and Firmicutes groups are detected by Toll-like receptor 5 (TLR5) in the host, triggering the innate immune response, and thus have been studied for the development of vaccines against diverse infections through fusion with protein antigens. However, H. pylori flagellin (hFlg) does not stimulate TLR5, allowing H. pylori to evade TLR5-mediated immune surveillance. The unresponsiveness of TLR5 to hFlg, along with the tendency of the hFlg protein to precipitate, limits the utility of hFlg for H. pylori vaccine development. Here, we report a soluble hFlg derivative protein that activates TLR5. We performed expression and purification screens with full-length and fragment hFlg proteins and identified the hypervariable domains as the soluble part of hFlg. The hypervariable domains of hFlg were engineered into a TLR5 agonist through fusion with the TLR5-activating Bacillus subtilis flagellin. Furthermore, based on comparative sequence and mutation analyses, we reveal that hFlg evolved to evade TLR5 detection by modifying residues that correspond to a TLR5-activation hot spot.

Crystal structure of the hydroxylaminopurine resistance protein, YiiM, and its putative molybdenum cofactor-binding catalytic site.

The molybdenum cofactor (Moco) is a molybdenum-conjugated prosthetic group that is ubiquitously found in plants, animals, and bacteria. Moco is required for the nitrogen-reducing reaction of the Moco sulfurase C-terminal domain (MOSC) family. Despite the biological significance of MOSC proteins in the conversion of prodrugs and resistance against mutagens, their structural features and Moco-mediated catalysis mechanism have not been described in detail. YiiM is a MOSC protein that is involved in reducing mutagenic 6-N-hydroxylaminopurine to nontoxic adenine in bacteria. Here, we report two crystal structures of YiiM: one from Gram-positive Geobacillus stearothermophilus (gsYiiM) and the other from Gram-negative Escherichia coli (ecYiiM). Although gsYiiM and ecYiiM differ in oligomerization state and protein stability, both consist of three structural modules (a ß-barrel and two α-helix bundles) and feature a cavity surrounded by the three modules. The cavity is characterized by positive electrostatic potentials and high sequence conservation. Moreover, the ecYiiM cavity houses a phosphate group, which emulates a part of Moco, and contains a highly reactive invariant cysteine residue. We thus propose that the cavity is the catalytic site where Moco binds and the substrate is reduced. Moreover, our comparative structural analysis highlights the common but distinct structural features of MOSC proteins.